Uses of Interface
info.bioinfweb.libralign.model.AlignmentModel

Packages that use AlignmentModel

Package	Description
info.bioinfweb.libralign.actions
info.bioinfweb.libralign.alignmentarea	Contains basic implementations for displaying an alignment area.
info.bioinfweb.libralign.dataarea	Contains DataArea from which all data areas used in LibrAlign must be inherited as well as related classes and a set of general data area implementations provided with LibrAlign which are located in the subpackage implementations.
info.bioinfweb.libralign.dataarea.implementations	Contains classes that implement a concrete data area.
info.bioinfweb.libralign.dataarea.implementations.charset	Contains data area related classes to display character sets of an alignment.
info.bioinfweb.libralign.dataarea.implementations.pherogram	Contains PherogramArea and other classes used in its implementation.
info.bioinfweb.libralign.dataarea.implementations.sequenceindex
info.bioinfweb.libralign.model	Contains the AlignmentModel interface which is the bridge between LibrAlign and any source of alignment data that is displayed with it as well as related classes and a set of implementations of this interface provided with LibrAlign.
info.bioinfweb.libralign.model.adapters	Contains adapter classes that allow to access the data provided by BasicAlignmentModelView in other ways (e.g.
info.bioinfweb.libralign.model.concatenated	Contains the interface ConcatenatedAlignmentModel and related implementations.
info.bioinfweb.libralign.model.events	Contains the event objects used by implementations of AlignmentModel.
info.bioinfweb.libralign.model.exception	Contains exceptions thrown by implementations of AlignmentModel.
info.bioinfweb.libralign.model.factory	Contains factory classes to create instances of implementations of AlignmentModel.
info.bioinfweb.libralign.model.factory.biojava	Contains alignment models working with BioJava Compounds.
info.bioinfweb.libralign.model.factory.continuous	Contains factories for alignment models that work with continuous values (e.g.
info.bioinfweb.libralign.model.implementations	Contains common implementations of AlignmentModel which are part of LibrAlign.
info.bioinfweb.libralign.model.implementations.decorate
info.bioinfweb.libralign.model.implementations.swingundo	Contains classes that allow to edit the underlying data source of an implementation of AlignmentModel using swing edit objects (implementations of UndoableEdit).
info.bioinfweb.libralign.model.io
info.bioinfweb.libralign.model.utils	Contains utility classes to be used with implementations of AlignmentModel.
info.bioinfweb.libralign.model.utils.indextranslation
info.bioinfweb.libralign.multiplealignments	Contains classes used in the implementation of MultipleAlignmentsContainer which allow to combine several AlignmentAreas.

Uses of AlignmentModel in info.bioinfweb.libralign.actions

Methods in info.bioinfweb.libralign.actions that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<T>	AlignmentActionProvider.getModel()

Uses of AlignmentModel in info.bioinfweb.libralign.alignmentarea

Methods in info.bioinfweb.libralign.alignmentarea that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<?>	AlignmentArea.getAlignmentModel() Returns the alignment model providing the data displayed by this area.
AlignmentModel<?>	AlignmentArea.setAlignmentModel(AlignmentModel<?> alignmentModel, boolean moveListeners) Changes the alignment model providing the data for this instance.

Methods in info.bioinfweb.libralign.alignmentarea with parameters of type AlignmentModel

Modifier and Type	Method and Description
<T,U> void	AlignmentArea.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)
<T,U> void	AlignmentArea.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)
AlignmentModel<?>	AlignmentArea.setAlignmentModel(AlignmentModel<?> alignmentModel, boolean moveListeners) Changes the alignment model providing the data for this instance.

Uses of AlignmentModel in info.bioinfweb.libralign.dataarea

Methods in info.bioinfweb.libralign.dataarea that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<?>	DataArea.getLabeledAlignmentModel() Convenience method that returns the alignment model of the labeled alignment area.

Methods in info.bioinfweb.libralign.dataarea with parameters of type AlignmentModel

Modifier and Type	Method and Description
<T,U> void	DataAreaSequenceChangeListener.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)
<T,U> void	DataAreaSequenceChangeListener.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)

Uses of AlignmentModel in info.bioinfweb.libralign.dataarea.implementations

Methods in info.bioinfweb.libralign.dataarea.implementations with parameters of type AlignmentModel

Modifier and Type	Method and Description
<T,U> void	LabelDataArea.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)
<T,U> void	LabelDataArea.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)
void	ConsensusSequenceArea.afterModelChanged(AlignmentModel previous, AlignmentModel current)
void	ConsensusSequenceArea.afterModelChanged(AlignmentModel previous, AlignmentModel current)

Uses of AlignmentModel in info.bioinfweb.libralign.dataarea.implementations.charset

Methods in info.bioinfweb.libralign.dataarea.implementations.charset with parameters of type AlignmentModel

Modifier and Type	Method and Description
<T,U> void	CharSetArea.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)
<T,U> void	CharSetArea.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)

Uses of AlignmentModel in info.bioinfweb.libralign.dataarea.implementations.pherogram

Methods in info.bioinfweb.libralign.dataarea.implementations.pherogram with parameters of type AlignmentModel

Modifier and Type	Method and Description
<T,U> void	PherogramArea.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)
<T,U> void	PherogramArea.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)

Uses of AlignmentModel in info.bioinfweb.libralign.dataarea.implementations.sequenceindex

Methods in info.bioinfweb.libralign.dataarea.implementations.sequenceindex with parameters of type AlignmentModel

Modifier and Type	Method and Description
<T,U> void	SequenceIndexArea.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)
<T,U> void	SequenceIndexArea.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)

Uses of AlignmentModel in info.bioinfweb.libralign.model

Subinterfaces of AlignmentModel in info.bioinfweb.libralign.model

Modifier and Type	Interface and Description
interface	AlignmentModelView<T,U> This interface should be implemented by all classes which return the contents of another implementation of AlignmentModel in a modified way.
interface	SequenceAccessAlignmentModel<S,T> Interface for classes implementing AlignmentModel by using sequence objects.

Methods in info.bioinfweb.libralign.model that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<T>	BasicAlignmentModelView.getUnderlyingModel() Returns the underlying sequence data provider that provides the data accessed with this object.

Methods in info.bioinfweb.libralign.model with parameters of type AlignmentModel

Modifier and Type	Method and Description
<T,U> void	AlignmentModelChangeAdapter.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)
<T,U> void	AlignmentModelChangeAdapter.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)
<T,U> void	AlignmentModelChangeListener.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current) Called if this listener was moved to another instance of AlignmentModel.
<T,U> void	AlignmentModelChangeListener.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current) Called if this listener was moved to another instance of AlignmentModel.

Uses of AlignmentModel in info.bioinfweb.libralign.model.adapters

Methods in info.bioinfweb.libralign.model.adapters that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<T>	AbstractBasicAlignmentModelView.getUnderlyingModel()

Methods in info.bioinfweb.libralign.model.adapters with parameters of type AlignmentModel

Modifier and Type	Method and Description
void	AbstractBasicAlignmentModelView.setUnderlyingModel(AlignmentModel<T> underlyingModel)

Constructors in info.bioinfweb.libralign.model.adapters with parameters of type AlignmentModel

Constructor and Description
AbstractBasicAlignmentModelView(AlignmentModel<T> underlyingModel)
AbstractSingleSequenceDataAdapter(AlignmentModel<T> underlyingModel, java.lang.String sequenceID) Creates a new instance of this class which views the whole length of a sequence in the underlying data source.
AbstractSingleSequenceDataAdapter(AlignmentModel<T> underlyingModel, java.lang.String sequenceID, int offset, int length) Creates a new instance of this class.
BioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider, org.biojava3.core.sequence.template.CompoundSet<C> compoundSet) Creates a new instance of this class.
CharSequenceAdapter(AlignmentModel<T> underlyingProvider, boolean cutLongRepresentations) Creates a new instance of this class.
SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider, java.lang.String sequenceID, org.biojava3.core.sequence.template.CompoundSet<C> compoundSet) Creates a new instance of this class that does not allow unknown compounds.
SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider, java.lang.String sequenceID, org.biojava3.core.sequence.template.CompoundSet<C> compoundSet, C unknownCompound) Creates a new instance of this class allowing unknown compounds.
SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider, java.lang.String sequenceID, int offset, int length, org.biojava3.core.sequence.template.CompoundSet<C> compoundSet) Creates a new instance of this class that does not allow unknown compounds.
SingleBioJava3SequenceAdapter(AlignmentModel<T> underlyingProvider, java.lang.String sequenceID, int offset, int length, org.biojava3.core.sequence.template.CompoundSet<C> compoundSet, C unknownCompound) Creates a new instance of this class allowing unknown compounds.
SingleCharSequenceAdapter(AlignmentModel<T> underlyingModel, java.lang.String sequenceID, boolean cutLongRepresentations) Creates a new instance of this class specifying a whole sequence to be viewed.
SingleCharSequenceAdapter(AlignmentModel<T> underlyingModel, java.lang.String sequenceID, int offset, int length, boolean cutLongRepresentations) Creates a new instance of this class specifying a subsequence to be viewed.
StringAdapter(AlignmentModel<T> underlyingProvider, boolean cutLongRepresentations) Creates a new instance of this class.

Uses of AlignmentModel in info.bioinfweb.libralign.model.concatenated

Subinterfaces of AlignmentModel in info.bioinfweb.libralign.model.concatenated

Modifier and Type	Interface and Description
interface	ConcatenatedAlignmentModel Warning: This interface is currently a placeholder.

Methods in info.bioinfweb.libralign.model.concatenated that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<?>	ConcatenatedAlignmentModel.getLastPartModel() Returns the right most part model contained in this alignment.
AlignmentModel<?>	ConcatenatedAlignmentModel.getPartModel(int index) Returns the part model at the specified position.
AlignmentModel<?>	ConcatenatedAlignmentModel.partModelByColumn(int columnIndex) Returns the part model currently responsible for providing the contents of the specified column.
AlignmentModel<?>	ConcatenatedAlignmentModel.removePartModel(int index) Removes the part model at the specified index from this concatenated alignment model.

Methods in info.bioinfweb.libralign.model.concatenated with parameters of type AlignmentModel

Modifier and Type	Method and Description
void	ConcatenatedAlignmentModel.appendPartModel(AlignmentModel<?> model) Appends an additional part model at the end of this concatenated alignment.
int	ConcatenatedAlignmentModel.columnOffsetForPartModel(AlignmentModel<?> partModel) Returns the global index of the first column provided by the specified part model.
boolean	ConcatenatedAlignmentModel.containsPartModel(AlignmentModel<?> partModel) Checks if the specified model is contained in this concatenated model.
void	ConcatenatedAlignmentModel.insertPartModel(int modelIndex, AlignmentModel<?> model) Inserts an additional part model at the specified position.
int	ConcatenatedAlignmentModel.partModelIndex(AlignmentModel<?> partModel) Returns the index of the specified part model in this concatenated alignment model.

Uses of AlignmentModel in info.bioinfweb.libralign.model.events

Methods in info.bioinfweb.libralign.model.events that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<T>	AlignmentModelChangeEvent.getSource() Returns the data provider where the change took place.

Methods in info.bioinfweb.libralign.model.events with parameters of type AlignmentModel

Modifier and Type	Method and Description
AlignmentModelChangeEvent<T>	AlignmentModelChangeEvent.cloneWithNewSource(AlignmentModel<T> source) Creates a copy of this event with all properties set to identical values but with a different source.
SequenceChangeEvent<T>	SequenceChangeEvent.cloneWithNewSource(AlignmentModel<T> source)
SequenceRenamedEvent<T>	SequenceRenamedEvent.cloneWithNewSource(AlignmentModel<T> source)
TokenChangeEvent<T>	TokenChangeEvent.cloneWithNewSource(AlignmentModel<T> source)
static <T> SequenceChangeEvent<T>	SequenceChangeEvent.newInsertInstance(AlignmentModel<T> source, java.lang.String sequenceID)
static <T> TokenChangeEvent<T>	TokenChangeEvent.newInsertInstance(AlignmentModel<T> source, java.lang.String sequenceID, int startIndex, java.util.Collection<? extends T> newTokens) Creates a new instance of this class that represents an insertion of a list of tokens.
static <T> TokenChangeEvent<T>	TokenChangeEvent.newInsertInstance(AlignmentModel<T> source, java.lang.String sequenceID, int index, T newToken) Creates a new instance of this class that represents an insertion of a single token.
static <T> SequenceChangeEvent<T>	SequenceChangeEvent.newRemoveInstance(AlignmentModel<T> source, java.lang.String sequenceID)
static <T> TokenChangeEvent<T>	TokenChangeEvent.newRemoveInstance(AlignmentModel<T> source, java.lang.String sequenceID, int startIndex, java.util.Collection<? extends T> removedTokens) Creates a new instance of this class that represents a deletion of a list of tokens.
static <T> TokenChangeEvent<T>	TokenChangeEvent.newRemoveInstance(AlignmentModel<T> source, java.lang.String sequenceID, int index, T removedToken) Creates a new instance of this class that represents a deletion of a single token.
static <T> TokenChangeEvent<T>	TokenChangeEvent.newReplaceInstance(AlignmentModel<T> source, java.lang.String sequenceID, int startIndex, java.util.Collection<? extends T> replacedTokens) Creates a new instance of this class that represents a replacement of a list of tokens.
static <T> TokenChangeEvent<T>	TokenChangeEvent.newReplaceInstance(AlignmentModel<T> source, java.lang.String sequenceID, int index, T replacedToken) Creates a new instance of this class that represents a replacement of a single token.

Constructors in info.bioinfweb.libralign.model.events with parameters of type AlignmentModel

Constructor and Description
AlignmentModelChangeEvent(AlignmentModel<T> source, java.lang.String sequenceID) Creates a new instance of this class.
SequenceChangeEvent(AlignmentModel<T> source, java.lang.String sequenceID, ListChangeType type)
SequenceRenamedEvent(AlignmentModel<T> source, java.lang.String sequenceID, java.lang.String previousName, java.lang.String newName)
TokenChangeEvent(AlignmentModel<T> source, java.lang.String sequenceID, ListChangeType type, int startIndex, java.util.Collection<? extends T> affectedTokens) Creates a new instance of this class.

Uses of AlignmentModel in info.bioinfweb.libralign.model.exception

Methods in info.bioinfweb.libralign.model.exception that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<?>	AlignmentModelException.getSource() Returns the instance of AlignmentModel that threw this exception.

Constructors in info.bioinfweb.libralign.model.exception with parameters of type AlignmentModel

Constructor and Description
AlignmentModelException(AlignmentModel<?> source)
AlignmentModelException(AlignmentModel<?> source, java.lang.String message)
AlignmentSourceNotWritableException(AlignmentModel<?> source)
InvalidTokenException(AlignmentModel<?> source, java.lang.Object token)
SequenceNotFoundException(AlignmentModel<?> source, java.lang.String sequenceID) Create a new instance of this class.

Uses of AlignmentModel in info.bioinfweb.libralign.model.factory

Methods in info.bioinfweb.libralign.model.factory that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<T>	AbstractAlignmentModelFactory.createNewModel(NewAlignmentModelParameterMap parameterMap)
AlignmentModel<T>	AlignmentModelFactory.createNewModel(NewAlignmentModelParameterMap parameterMap) Creates a new instance of an alignment model according to the specified parameters.
AlignmentModel<java.lang.String>	StringAlignmentModelFactory.createNewModel(NewAlignmentModelParameterMap parameterMap) Creates a new instance of PackedAlignmentModel if the number of tokens is specified (using NewAlignmentModelParameterMap.KEY_CHARACTER_STATE_COUNT) or ArrayListAlignmentModel if not.
protected abstract AlignmentModel<T>	AbstractAlignmentModelFactory.doCreateNewModel(NewAlignmentModelParameterMap parameterMap)
AlignmentModel<java.lang.Character>	BioPolymerCharAlignmentModelFactory.doCreateNewModel(NewAlignmentModelParameterMap parameterMap)

Methods in info.bioinfweb.libralign.model.factory with parameters of type AlignmentModel

Modifier and Type	Method and Description
java.lang.Character	BioPolymerCharAlignmentModelFactory.createToken(AlignmentModel<java.lang.Character> alignmentModel, java.lang.String tokenRepresentation)
java.lang.String	StringAlignmentModelFactory.createToken(AlignmentModel<java.lang.String> alignmentModel, java.lang.String tokenRepresentation) Creates the token using the token set of the specified alignment model.
T	AbstractAlignmentModelFactory.createToken(AlignmentModel<T> alignmentModel, java.lang.String tokenRepresentation) Creates a token using TokenSet.tokenByRepresentation(String).
T	AlignmentModelFactory.createToken(AlignmentModel<T> alignmentModel, java.lang.String tokenRepresentation) Creates a token object associated with the specified string representation.

Uses of AlignmentModel in info.bioinfweb.libralign.model.factory.biojava

Methods in info.bioinfweb.libralign.model.factory.biojava that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<org.biojava3.core.sequence.compound.AminoAcidCompound>	BioJava3AminoAcidAligmentModelFactory.createNewModel(NewAlignmentModelParameterMap parameterMap)
AlignmentModel<org.biojava3.core.sequence.compound.NucleotideCompound>	BioJava3NucleotideAlignmentModelFactory.createNewModel(NewAlignmentModelParameterMap parameterMap)

Methods in info.bioinfweb.libralign.model.factory.biojava with parameters of type AlignmentModel

Modifier and Type	Method and Description
org.biojava3.core.sequence.compound.AminoAcidCompound	BioJava3AminoAcidAligmentModelFactory.createToken(AlignmentModel<org.biojava3.core.sequence.compound.AminoAcidCompound> alignmentModel, java.lang.String tokenRepresentation) Creates the token using the token set of the specified alignment model.
org.biojava3.core.sequence.compound.NucleotideCompound	BioJava3NucleotideAlignmentModelFactory.createToken(AlignmentModel<org.biojava3.core.sequence.compound.NucleotideCompound> alignmentModel, java.lang.String tokenRepresentation)

Uses of AlignmentModel in info.bioinfweb.libralign.model.factory.continuous

Methods in info.bioinfweb.libralign.model.factory.continuous that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<ContinuousToken<java.lang.Double>>	DoubleAlignmentModelFactory.doCreateNewModel(NewAlignmentModelParameterMap parameterMap)
AlignmentModel<ContinuousToken<java.lang.Float>>	FloatAlignmentModelFactory.doCreateNewModel(NewAlignmentModelParameterMap parameterMap)

Uses of AlignmentModel in info.bioinfweb.libralign.model.implementations

Classes in info.bioinfweb.libralign.model.implementations with type parameters of type AlignmentModel

Modifier and Type	Class and Description
class	AbstractSequenceIDIterator<P extends AlignmentModel> Abstract implementation of an iterator returning the IDs of all sequences provided by an implementation of AlignmentModel.

Classes in info.bioinfweb.libralign.model.implementations that implement AlignmentModel

Modifier and Type	Class and Description
class	AbstractAlignmentModel<T> This is the base class for all alignment models and alignment model decorators.
class	AbstractListAlignmentModel<T> An abstract implementation of AlignmentModel using a map of lists to store alignment data.
class	AbstractMapBasedAlignmentModel<S,T> Implements all methods dealing with the organization of the sequence set using some implementation of Map to identify the sequence object belonging to a sequence ID.
class	AbstractUndecoratedAlignmentModel<T> Implements general functionality for alignment models that are not decorators of other models.
class	AbstractUnmodifyableAlignmentModel<S,T> Implements basic functionality for a map based alignment model that uses unmodifiable sequence objects as its underlying data source.
class	ArrayListAlignmentModel<T> An implementation of AlignmentModel using a map of array lists to store alignment data.
class	BioJava3SequenceAlignmentModel<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound> /** An implementation of AlignmentModel backed by a set of BioJava Sequence implementations.
class	CharSequenceAlignmentModel An implementation of AlignmentModel backed by a set of CharSequence implementations (e.g.
class	PackedAlignmentModel<T> An alignment model using a PackedObjectArrayList as the underlying data source.

Methods in info.bioinfweb.libralign.model.implementations with parameters of type AlignmentModel

Modifier and Type	Method and Description
java.lang.String	SequenceIDManager.renameSequence(java.lang.String sequenceID, java.lang.String newSequenceName, AlignmentModel<?> model) Renames a sequence in the underlying data source.

Uses of AlignmentModel in info.bioinfweb.libralign.model.implementations.decorate

Classes in info.bioinfweb.libralign.model.implementations.decorate that implement AlignmentModel

Modifier and Type	Class and Description
class	AbstractAlignmentModelDecorator<T,U> Basic implementation of AlignmentModelView which delegates sequence specific methods (which are independent of the token type) to the underlying model.
class	AbstractTokenReplacementAlignmentModelDecorator<T,U> Abstract base class for implementations of AlignmentModelView that simply replace a set of tokens by other tokens of the same type.
class	DelegatedAlignmentModelView<T> Implementation of AlignmentModelView that delegates all methods to the underlying model and uses the same token type as the underlying model.
class	DNAAlignmentModelDecorator<T,U> Shows the underlying nucleotide data source as a DNA sequence, i.e.
class	RNAAlignmentModelDecorator<T,U> Shows the underlying nucleotide data source as a RNA sequence, i.e.

Methods in info.bioinfweb.libralign.model.implementations.decorate that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<U>	AbstractAlignmentModelDecorator.getUnderlyingModel()

Methods in info.bioinfweb.libralign.model.implementations.decorate with parameters of type AlignmentModel

Modifier and Type	Method and Description
static DNAAlignmentModelDecorator<java.lang.Character,java.lang.Character>	DNAAlignmentModelDecorator.newCharacterInstance(AlignmentModel<java.lang.Character> underlyingModel)
static RNAAlignmentModelDecorator<java.lang.Character,java.lang.Character>	RNAAlignmentModelDecorator.newCharacterInstance(AlignmentModel<java.lang.Character> underlyingModel)
protected void	AbstractAlignmentModelDecorator.setUnderlyingModel(AlignmentModel<U> underlyingModel) Replaces the decorated (underlying) model.

Constructors in info.bioinfweb.libralign.model.implementations.decorate with parameters of type AlignmentModel

Constructor and Description
AbstractAlignmentModelDecorator(TokenSet<T> tokenSet, AlignmentModel<U> underlyingModel) Creates a new instance of this class.
AbstractTokenReplacementAlignmentModelDecorator(TokenSet<T> tokenSet, AlignmentModel<U> underlyingModel) Creates a new instance of this class.
DelegatedAlignmentModelView(AlignmentModel<T> underlyingModel)
DNAAlignmentModelDecorator(TokenSet<T> tokenSet, AlignmentModel<U> underlyingModel)
RNAAlignmentModelDecorator(TokenSet<T> tokenSet, AlignmentModel<U> underlyingModel)

Uses of AlignmentModel in info.bioinfweb.libralign.model.implementations.swingundo

Classes in info.bioinfweb.libralign.model.implementations.swingundo that implement AlignmentModel

Modifier and Type	Class and Description
class	SwingUndoAlignmentModel<T> An implementation of AlignmentModel that creates an UndoableEdit object for every modification that is made to the underlying data source using any of the methods specified by AlignmentModel.

Fields in info.bioinfweb.libralign.model.implementations.swingundo declared as AlignmentModel

Modifier and Type	Field and Description
protected AlignmentModel<T>	SwingUndoAlignmentModel.underlyingModel

Methods in info.bioinfweb.libralign.model.implementations.swingundo that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<T>	SwingUndoAlignmentModel.getUnderlyingModel() Returns the underlying sequence data provider used to perform the actual manipulation of the data.

Constructors in info.bioinfweb.libralign.model.implementations.swingundo with parameters of type AlignmentModel

Constructor and Description
SwingUndoAlignmentModel(AlignmentModel<T> underlyingModel, javax.swing.undo.UndoManager undoManager) Creates a new instance of this class which creates default LibrAlign edit objects.
SwingUndoAlignmentModel(AlignmentModel<T> underlyingModel, javax.swing.undo.UndoManager undoManager, SwingEditFactory<T> editFactory) Creates a new instance of this class which creates new edit objects using the provided SwingEditFactory.

Uses of AlignmentModel in info.bioinfweb.libralign.model.io

Methods in info.bioinfweb.libralign.model.io that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<?>	AlignmentModelEventReader.getCurrentModel() Returns the alignment model that is currently read.
AlignmentModel<?>	AlignmentModelEventReader.getModelByJPhyloIOID(java.lang.String id) Returns the alignment model associated with the specified JPhyloIO ID.

Methods in info.bioinfweb.libralign.model.io that return types with arguments of type AlignmentModel

Modifier and Type	Method and Description
java.util.List<AlignmentModel<?>>	AlignmentModelEventReader.getCompletedModels() Returns the list of alignment models that have been completely read from the underlying JPhyloIO event stream until now.
static java.util.List<AlignmentModel<?>>	IOTools.readAlignments(java.io.File file) Reads a set of alignments from a file into a list of alignment model instances.
static java.util.List<AlignmentModel<?>>	IOTools.readAlignments(java.io.File file, info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) Reads a set of alignments from a file into a list of alignment model instances.

Methods in info.bioinfweb.libralign.model.io with parameters of type AlignmentModel

Modifier and Type	Method and Description
static <T> info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter	IOTools.createDocumentAdapter(AlignmentModel<T> model) Creates a document data adapter that allows to write the contents of model to a file using e.g.
static <T> info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter	IOTools.createDocumentAdapter(AlignmentModel<T> model, java.lang.String alignmentLabel) Creates a document data adapter that allows to write the contents of model to a file using e.g.
static <T> info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter	IOTools.createDocumentAdapter(AlignmentModel<T> model, java.lang.String alignmentLabel, boolean linkOTUs) Creates a document data adapter that allows to write the contents of model to a file using e.g.
static <T> void	IOTools.writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.File file, java.lang.String format) Writes the contents of an alignment model to a file in the specified format.
static <T> void	IOTools.writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.File file, java.lang.String format, info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) Writes the contents of an alignment model to a file in the specified format.
static <T> void	IOTools.writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.OutputStream stream, java.lang.String format) Writes the contents of an alignment model to a file in the specified format.
static <T> void	IOTools.writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.OutputStream stream, java.lang.String format, info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) Writes the contents of an alignment model to a file in the specified format.
static <T> void	IOTools.writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.Writer writer, java.lang.String format) Writes the contents of an alignment model to a file in the specified format.
static <T> void	IOTools.writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.Writer writer, java.lang.String format, info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) Writes the contents of an alignment model to a file in the specified format.

Constructors in info.bioinfweb.libralign.model.io with parameters of type AlignmentModel

Constructor and Description
AlignmentModelDataAdapter(java.lang.String idPrefix, info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent startEvent, AlignmentModel<T> model, boolean linkOTUs) Creates a new instance of this class.

Uses of AlignmentModel in info.bioinfweb.libralign.model.utils

Methods in info.bioinfweb.libralign.model.utils with parameters of type AlignmentModel

Modifier and Type	Method and Description
static void	AlignmentModelUtils.reverseComplement(AlignmentModel<?> model, java.lang.String sequenceID) Reverse complements a whole nucleotide sequence.
static <T> void	AlignmentModelUtils.reverseComplement(AlignmentModel<T> model, java.lang.String sequenceID, int start, int end) Reverse complements a part of a nucleotide sequence.

Uses of AlignmentModel in info.bioinfweb.libralign.model.utils.indextranslation

Methods in info.bioinfweb.libralign.model.utils.indextranslation that return AlignmentModel

Modifier and Type	Method and Description
AlignmentModel<T>	AbstractIndexTranslator.getModel()
AlignmentModel<T>	IndexTranslator.getModel() Returns the alignment model this instance works on.

Constructors in info.bioinfweb.libralign.model.utils.indextranslation with parameters of type AlignmentModel

Constructor and Description
AbstractIndexTranslator(AlignmentModel<T> model, java.util.Set<T> gapTokens)
RandomAccessIndexTranslator(AlignmentModel<T> model) Creates a new instance of this class using a HashSet containing the gap token specified by the token set of model.
RandomAccessIndexTranslator(AlignmentModel<T> model, java.util.Set<T> gapTokens)

Uses of AlignmentModel in info.bioinfweb.libralign.multiplealignments

Methods in info.bioinfweb.libralign.multiplealignments with parameters of type AlignmentModel

Modifier and Type	Method and Description
<T,U> void	MultipleAlignmentsModelEventForwarder.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)
<T,U> void	MultipleAlignmentsModelEventForwarder.afterModelChanged(AlignmentModel<T> previous, AlignmentModel<U> current)